Radiographs are used as the most important imaging tool for identifying spine anomalies in clinical practice. The evaluation of spinal bone lesions, however, is a challenging task for radiologists. This work aims at developing and evaluating a deep learning-based framework, named VinDr-SpineXR, for the classification and localization of abnormalities from spine X-rays. First, we build a large dataset, comprising 10,468 spine X-ray images from 5,000 studies, each of which is manually annotated by an experienced radiologist with bounding boxes around abnormal findings in 13 categories. Using this dataset, we then train a deep learning classifier to determine whether a spine scan is abnormal and a detector to localize 7 crucial findings amongst the total 13. The VinDr-SpineXR is evaluated on a test set of 2,078 images from 1,000 studies, which is kept separate from the training set. It demonstrates an area under the receiver operating characteristic curve (AUROC) of 88.61% (95% CI 87.19%, 90.02%) for the image-level classification task and a mean average precision (mAP@0.5) of 33.56% for the lesion-level localization task. These results serve as a proof of concept and set a baseline for future research in this direction. To encourage advances, the dataset, codes, and trained deep learning models are made publicly available.
Tyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical significance and prognostic values of the tyrosine catabolic genes in HCC. We find that five tyrosine catabolic enzymes are downregulated in HCC compared to normal liver at mRNA and protein level. Moreover, low expression of these enzymes correlates with poorer survival in patients with HCC. Notably, we identify pathways and upstream regulators that might involve in tyrosine catabolic reprogramming and further drive HCC development. In total, our results underscore tyrosine metabolism alteration in HCC and lay foundation for incorporating these pathway components in therapeutics and preventative strategies.
Recent years have experienced phenomenal growth in computer-aided diagnosis systems based on machine learning algorithms for anomaly detection tasks in the medical image domain. However, the performance of these algorithms greatly depends on the quality of labels since the subjectivity of a single annotator might decline the certainty of medical image datasets. In order to alleviate this problem, aggregating labels from multiple radiologists with different levels of expertise has been established. In particular, under the reliance on their own biases and proficiency levels, different qualified experts provide their estimations of the "true" bounding boxes representing the anomaly observations. Learning from these nonstandard labels exerts negative effects on the performance of machine learning networks. In this paper, we propose a simple yet effective approach for the enhancement of neural networks' efficiency in abnormal detection tasks by estimating the actually hidden labels from multiple ones. A re-weighted loss function is also used to improve the detection capacity of the networks. We conduct an extensive experimental evaluation of our proposed approach on both simulated and real-world medical imaging datasets, MED-MNIST and VinDr-CXR. The experimental results show that our approach is able to capture the reliability of different annotators and outperform relevant baselines that do not consider the disagreements among annotators. Our code is available at https://github.com/huyhieupham/learning-from-multiple-annotators.
We propose a vector space approach for inverse rendering of a Lambertian convex object with distant light sources. In this problem, the texture of the object and arbitrary lightings are both to be recovered from multiple images of the object and its 3D model. Our work is motivated by the observation that all possible images of a Lambertian object lie around a low-dimensional linear subspace spanned by the first few spherical harmonics. The inverse rendering can therefore be formulated as a matrix factorization, in which the basis of the subspace is encoded in a spherical harmonic matrix S associated with the object’s geometry. A necessary and sufficient condition on S for unique factorization is derived with an introduction to a new notion of matrix rank called nonseparable full rank. A singular value decomposition-based algorithm for exact factorization in the noiseless case is introduced. In the presence of noise, two algorithms, namely, alternating and optimization based are proposed to deal with two different types of noise. A random sample consensus-based algorithm is introduced to reduce the size of the optimization problem, which is equal to the number of pixels in each image. Implementations of the proposed algorithms are done on a real data set.
We conducted a prospective study to measure the clinical impact of an explainable machine learning system on interobserver agreement in chest radiograph interpretation. The AI system, which we call as it VinDr-CXR when used as a diagnosis-supporting tool, significantly improved the agreement between six radiologists with an increase of 1.5% in mean Fleiss' Kappa. In addition, we also observed that, after the radiologists consulted AI's suggestions, the agreement between each radiologist and the system was remarkably increased by 3.3% in mean Cohen's Kappa. This work has been accepted for publication in IEEE Access and this paper is our short version submitted to the Midwest Machine Learning Symposium (MMLS 2023), Chicago, IL, USA.
Abstract Chest radiograph (CXR) interpretation is critical for the diagnosis of various thoracic diseases in pediatric patients. This task, however, is error-prone and requires a high level of understanding of radiologic expertise. Recently, deep convolutional neural networks (D-CNNs) have shown remarkable performance in interpreting CXR in adults. However, there is a lack of evidence indicating that D-CNNs can recognize accurately multiple lung pathologies from pediatric CXR scans. In particular, the development of diagnostic models for the detection of pediatric chest diseases faces significant challenges such as ( i ) lack of physician-annotated datasets and ( ii ) class imbalance problems. In this paper, we retrospectively collect a large dataset of 5,017 pediatric CXR scans, for which each is manually labeled by an experienced radiologist for the presence of 10 common pathologies. A D-CNN model is then trained on 3,550 annotated scans to classify multiple pediatric lung pathologies automatically. To address the highclass imbalance issue, we propose to modify and apply “Distribution-Balanced loss” for training D-CNNs which reshapes the standard Binary-Cross Entropy loss (BCE) to efficiently learn harder samples by down-weighting the loss assigned to the majority classes. On an independent test set of 777 studies, the proposed approach yields an area under the receiver operating characteristic (AUC) of 0.709 (95% CI, 0.690–0.729). The sensitivity, specificity, and F1-score at the cutoff value are 0.722 (0.694–0.750), 0.579 (0.563–0.595), and 0.389 (0.373–0.405), respectively. These results significantly outperform previous state-of-the-art methods on most of the target diseases. Moreover, our ablation studies validate the effectiveness of the proposed loss function compared to other standard losses, e.g., BCE and Focal Loss, for this learning task. Overall, we demonstrate the potential of D-CNNs in interpreting pediatric CXRs.
In 2008, M. Marshall settled a long-standing open problem by showing that if f(x,y) is a polynomial that is non-negative on the strip [0,1] x R, then there exist sums of squares s(x,y) and t(x,y) such that f(x,y) = s(x,y) + (x - x^2) t(x,y). In this paper, we generalize Marshall's result to various strips and half-strips in the plane. Our results give many new examples of non-compact semialgebraic sets in R^2 for which one can characterize all polynomials which are non-negative on the set. For example, we show that if U is a compact set in the real line and {g_1, ..., g_k} a specific set of generators for U as a semialgebraic set, then whenever f(x,y) is non-negative on U x R, there are sums of squares s_0, ..., s_k such that f = s_0 + s_1 g_1 + ... + s_k g_k.
The Poisson summation formula (PSF), which relates the sampling of an analog signal with the periodization of its Fourier transform, plays a key role in the classical sampling theory. In its current forms, the formula is only applicable to a limited class of signals in L 1 . However, this assumption on the signals is too strict for many applications in signal processing that require sampling of non-decaying signals. In this paper we generalize the PSF for functions living in weighted Sobolev spaces that do not impose any decay on the functions. The only requirement is that the signal to be sampled and its weak derivatives up to order 1/2+ ε for arbitrarily small ε > 0, grow slower than a polynomial in the L 2 sense. The generalized PSF will be interpreted in the language of distributions.
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